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- PDB-2m11: Structure of perimidinone-derived synthetic nucleoside paired wit... -
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Basic information
Entry | Database: PDB / ID: 2m11 | ||||||||||||||||||||||
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Title | Structure of perimidinone-derived synthetic nucleoside paired with guanine in DNA duplex | ||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / B-form DNA / dPer / Perimidinone-Derived Nucleoside / Dickerson-Drew Dodecamer | Function / homology | DNA / DNA (> 10) | ![]() Method | SOLUTION NMR / simulated annealing | Model details | mean structure, model1 | Model type details | minimized average | ![]() Kowal, E.A. / Lad, R. / Pallan, P.S. / Muffly, E. / Wawrzak, Z. / Egli, M. / Sturla, S.J. / Stone, M.P. | ![]() ![]() Title: Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction. Authors: Kowal, E.A. / Lad, R.R. / Pallan, P.S. / Dhummakupt, E. / Wawrzak, Z. / Egli, M. / Sturla, S.J. / Stone, M.P. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.2 KB | Display | ![]() |
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PDB format | ![]() | 130.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 336.7 KB | Display | ![]() |
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Full document | ![]() | 427 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 15.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: DNA chain | Mass: 3736.484 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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Sample preparation
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Sample |
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Sample conditions |
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-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 153 | ||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: back calculated data agree with experimental NOESY spectrum Conformers calculated total number: 10 / Conformers submitted total number: 10 |